Variant report

Variant	rs1123269
Chromosome Location	chr2:9886035-9886036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:9877830..9880619-chr2:9884575..9886353,2	MCF-7	breast:
2	chr2:9877832..9879861-chr2:9884355..9886742,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10171491	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10173057	0.90[ASN][1000 genomes]
rs10176382	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10178017	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10180724	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10200779	0.90[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10200869	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10202283	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929607	0.86[ASN][1000 genomes]
rs10929608	0.86[ASN][1000 genomes]
rs10929609	0.86[ASN][1000 genomes]
rs1110317	0.87[ASN][1000 genomes]
rs11674024	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11674642	0.90[JPT][hapmap]
rs11676286	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678697	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11680429	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs12470409	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12475853	0.89[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12476199	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692393	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12692394	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12996417	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13018695	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13023725	0.81[ASN][1000 genomes]
rs13028425	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13395171	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398163	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398193	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398304	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1554107	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554108	0.84[ASN][1000 genomes]
rs2357263	0.90[CEU][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap]
rs34491197	0.83[ASN][1000 genomes]
rs4668636	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4668637	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4668644	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4669427	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4669428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4669429	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs4669445	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs4669447	0.86[ASN][1000 genomes]
rs4669448	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4669451	0.85[ASN][1000 genomes]
rs6432033	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6708081	0.85[ASN][1000 genomes]
rs6713497	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732548	0.81[ASN][1000 genomes]
rs6735280	0.90[JPT][hapmap]
rs6740013	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6742929	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6743152	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6754662	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6756567	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6761286	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6761920	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7423455	0.89[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7423458	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602784	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs7605675	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs868442	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1123269	PDIA6	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9880200-9892800	Weak transcription	Thymus	Thymus
2	chr2:9880200-9893200	Weak transcription	Right Atrium	heart
3	chr2:9884200-9886400	Enhancers	Pancreas	Pancrea
4	chr2:9884600-9886600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:9884800-9892600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:9885200-9886200	Weak transcription	Fetal Heart	heart
7	chr2:9885200-9888400	Weak transcription	Fetal Intestine Small	intestine
8	chr2:9885200-9891200	Weak transcription	Right Ventricle	heart
9	chr2:9885200-9891400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:9885200-9893000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:9885400-9887600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:9885400-9888600	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:9885400-9888800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr2:9885400-9888800	Weak transcription	Hela-S3	cervix
15	chr2:9885400-9891000	Weak transcription	Psoas Muscle	Psoas
16	chr2:9885400-9893000	Weak transcription	Left Ventricle	heart
17	chr2:9885600-9888200	Weak transcription	Fetal Intestine Large	intestine
18	chr2:9885600-9888400	Weak transcription	A549	lung
19	chr2:9885600-9888600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:9885600-9888600	Weak transcription	HSMM	muscle
21	chr2:9885600-9888800	Weak transcription	HMEC	breast
22	chr2:9885600-9889000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:9885600-9892600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:9885800-9886200	Enhancers	Spleen	Spleen
25	chr2:9885800-9887800	Enhancers	Fetal Muscle Trunk	muscle
26	chr2:9885800-9891000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:9885800-9891600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:9886000-9886200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:9886000-9891600	Weak transcription	NHDF-Ad	bronchial

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